venncommand.cpp

   1 /*
   2  *  venncommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/30/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "venncommand.h"
  11 #include "ace.h"
  12 #include "sobs.h"
  13 #include "chao1.h"
  14 //#include "jackknife.h"
  15 #include "sharedsobscollectsummary.h"
  16 #include "sharedchao1.h"
  17 #include "sharedace.h"
  18 #include "nseqs.h"
  19
  20
  21 //**********************************************************************************************************************
  22
  23 VennCommand::VennCommand(string option)  {
  24         try {
  25                 globaldata = GlobalData::getInstance();
  26                 abort = false;
  27                 allLines = 1;
  28                 labels.clear();
  29
  30                 //allow user to run help
  31                 if(option == "help") { help(); abort = true; }
  32
  33                 else {
  34                         //valid paramters for this command
  35                         string AlignArray[] =  {"groups","label","calc","permute", "abund","nseqs","outputdir","inputdir"};
  36                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  37
  38                         OptionParser parser(option);
  39                         map<string,string> parameters = parser.getParameters();
  40
  41                         ValidParameters validParameter;
  42
  43                         //check to make sure all parameters are valid for command
  44                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  45                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  46                         }
  47
  48                         //make sure the user has already run the read.otu command
  49                         if ((globaldata->getListFile() == "") && (globaldata->getSharedFile() == "")) {
  50                                 m->mothurOut("You must read a list, or a list and a group, or a shared before you can use the venn command."); m->mothurOutEndLine(); abort = true;
  51                         }
  52
  53                         //if the user changes the output directory command factory will send this info to us in the output parameter
  54                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){
  55                                 outputDir = "";
  56                                 outputDir += m->hasPath(globaldata->inputFileName); //if user entered a file with a path then preserve it
  57                         }
  58
  59                         //check for optional parameter and set defaults
  60                         // ...at some point should added some additional type checking...
  61                         label = validParameter.validFile(parameters, "label", false);
  62                         if (label == "not found") { label = ""; }
  63                         else {
  64                                 if(label != "all") {  m->splitAtDash(label, labels);  allLines = 0;  }
  65                                 else { allLines = 1;  }
  66                         }
  67
  68                         //if the user has not specified any labels use the ones from read.otu
  69                         if (label == "") {
  70                                 allLines = globaldata->allLines;
  71                                 labels = globaldata->labels;
  72                         }
  73
  74                         groups = validParameter.validFile(parameters, "groups", false);
  75                         if (groups == "not found") { groups = ""; }
  76                         else {
  77                                 m->splitAtDash(groups, Groups);
  78                                 globaldata->Groups = Groups;
  79                         }
  80
  81                         format = globaldata->getFormat();
  82                         calc = validParameter.validFile(parameters, "calc", false);
  83                         if (calc == "not found") {
  84                                 if(format == "list") { calc = "sobs"; }
  85                                 else { calc = "sharedsobs"; }
  86                         }
  87                         else {
  88                                  if (calc == "default")  {
  89                                         if(format == "list") { calc = "sobs"; }
  90                                         else { calc = "sharedsobs"; }
  91                                 }
  92                         }
  93                         m->splitAtDash(calc, Estimators);
  94
  95                         string temp;
  96                         temp = validParameter.validFile(parameters, "abund", false);            if (temp == "not found") { temp = "10"; }
  97                         convert(temp, abund);
  98
  99                         temp = validParameter.validFile(parameters, "nseqs", false);            if (temp == "not found"){       temp = "f";                             }
 100                         nseqs = m->isTrue(temp);
 101
 102                         temp = validParameter.validFile(parameters, "permute", false);                  if (temp == "not found"){       temp = "f";                             }
 103                         perm = m->isTrue(temp);
 104
 105                         if (abort == false) {
 106                                 validCalculator = new ValidCalculators();
 107
 108                                 int i;
 109
 110                                 if (format == "list") {
 111                                         for (i=0; i<Estimators.size(); i++) {
 112                                                 if (validCalculator->isValidCalculator("vennsingle", Estimators[i]) == true) {
 113                                                         if (Estimators[i] == "sobs") {
 114                                                                 vennCalculators.push_back(new Sobs());
 115                                                         }else if (Estimators[i] == "chao") {
 116                                                                 vennCalculators.push_back(new Chao1());
 117                                                         }else if (Estimators[i] == "ace") {
 118                                                                 if(abund < 5)
 119                                                                         abund = 10;
 120                                                                 vennCalculators.push_back(new Ace(abund));
 121                                                         }
 122                                                 }
 123                                         }
 124                                 }else {
 125                                         for (i=0; i<Estimators.size(); i++) {
 126                                                 if (validCalculator->isValidCalculator("vennshared", Estimators[i]) == true) {
 127                                                         if (Estimators[i] == "sharedsobs") {
 128                                                                 vennCalculators.push_back(new SharedSobsCS());
 129                                                         }else if (Estimators[i] == "sharedchao") {
 130                                                                 vennCalculators.push_back(new SharedChao1());
 131                                                         }else if (Estimators[i] == "sharedace") {
 132                                                                 vennCalculators.push_back(new SharedAce());
 133                                                         }
 134                                                 }
 135                                         }
 136                                 }
 137
 138                                 //if the users entered no valid calculators don't execute command
 139                                 if (vennCalculators.size() == 0) { m->mothurOut("No valid calculators given, please correct."); m->mothurOutEndLine(); abort = true;  }
 140                                 else {  venn = new Venn(outputDir, nseqs);  }
 141                         }
 142
 143                 }
 144
 145
 146
 147         }
 148         catch(exception& e) {
 149                 m->errorOut(e, "VennCommand", "VennCommand");
 150                 exit(1);
 151         }
 152 }
 153
 154 //**********************************************************************************************************************
 155
 156 void VennCommand::help(){
 157         try {
 158                 m->mothurOut("The venn command can only be executed after a successful read.otu command.\n");
 159                 m->mothurOut("The venn command parameters are groups, calc, abund, nseqs, permute and label.  No parameters are required.\n");
 160                 m->mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your venn diagram, you may only use a maximum of 4 groups.\n");
 161                 m->mothurOut("The group names are separated by dashes. The label allows you to select what distance levels you would like a venn diagram created for, and are also separated by dashes.\n");
 162                 m->mothurOut("The venn command should be in the following format: venn(groups=yourGroups, calc=yourCalcs, label=yourLabels, abund=yourAbund).\n");
 163                 m->mothurOut("Example venn(groups=A-B-C, calc=sharedsobs-sharedchao, abund=20).\n");
 164                 m->mothurOut("The default value for groups is all the groups in your groupfile up to 4, and all labels in your inputfile will be used.\n");
 165                 m->mothurOut("The default value for calc is sobs if you have only read a list file or if you have selected only one group, and sharedsobs if you have multiple groups.\n");
 166                 m->mothurOut("The default available estimators for calc are sobs, chao and ace if you have only read a list file, and sharedsobs, sharedchao and sharedace if you have read a list and group file or a shared file.\n");
 167                 m->mothurOut("The nseqs parameter will output the number of sequences represented by the otus in the picture, default=F.\n");
 168                 m->mothurOut("If you have more than 4 groups, the permute parameter will find all possible combos of 4 of your groups and create pictures for them, default=F.\n");
 169                 m->mothurOut("The only estimators available four 4 groups are sharedsobs and sharedchao.\n");
 170                 m->mothurOut("The venn command outputs a .svg file for each calculator you specify at each distance you choose.\n");
 171                 m->mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 172         }
 173         catch(exception& e) {
 174                 m->errorOut(e, "VennCommand", "help");
 175                 exit(1);
 176         }
 177 }
 178
 179
 180 //**********************************************************************************************************************
 181
 182 VennCommand::~VennCommand(){
 183         if (abort == false) {
 184                 delete input; globaldata->ginput = NULL;
 185                 delete read;
 186                 delete venn;
 187                 globaldata->sabund = NULL;
 188                 delete validCalculator;
 189         }
 190
 191 }
 192
 193 //**********************************************************************************************************************
 194
 195 int VennCommand::execute(){
 196         try {
 197
 198                 if (abort == true) { return 0; }
 199
 200                 string lastLabel;
 201                 vector<string> outputNames;
 202
 203                 if (format == "sharedfile") {
 204                         //you have groups
 205                         read = new ReadOTUFile(globaldata->inputFileName);
 206                         read->read(&*globaldata);
 207
 208                         input = globaldata->ginput;
 209                         lookup = input->getSharedRAbundVectors();
 210                         lastLabel = lookup[0]->getLabel();
 211
 212                         if ((lookup.size() > 4) && (perm)) { combosOfFour = findCombinations(lookup.size()); }
 213                 }else if (format == "list") {
 214                         //you are using just a list file and have only one group
 215                         read = new ReadOTUFile(globaldata->inputFileName);
 216                         read->read(&*globaldata);
 217
 218                         sabund = globaldata->sabund;
 219                         lastLabel = sabund->getLabel();
 220                         input = globaldata->ginput;
 221                 }
 222
 223                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 224                 set<string> processedLabels;
 225                 set<string> userLabels = labels;
 226
 227                 if (format != "list") {
 228
 229                         //as long as you are not at the end of the file or done wih the lines you want
 230                         while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 231
 232                                 if (m->control_pressed) {
 233                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 234                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 235                                         globaldata->Groups.clear();
 236                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 237                                         return 0;
 238                                 }
 239
 240                                 if(allLines == 1 || labels.count(lookup[0]->getLabel()) == 1){
 241                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 242                                         processedLabels.insert(lookup[0]->getLabel());
 243                                         userLabels.erase(lookup[0]->getLabel());
 244
 245                                         if ((lookup.size() > 4) && (!perm)){
 246                                                 m->mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 247                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 248
 249                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 250                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 251
 252                                         }else if ((lookup.size() > 4) && (perm)) {
 253                                                 set< set<int> >::iterator it3;
 254                                                 set<int>::iterator it2;
 255                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 256
 257                                                         set<int> poss = *it3;
 258                                                         vector<SharedRAbundVector*> subset;
 259                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 260
 261                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 262                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 263                                                 }
 264                                         }else {
 265                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 266                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 267                                         }
 268                                 }
 269
 270                                 if ((m->anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 271                                         string saveLabel = lookup[0]->getLabel();
 272
 273                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 274                                         lookup = input->getSharedRAbundVectors(lastLabel);
 275
 276                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 277                                         processedLabels.insert(lookup[0]->getLabel());
 278                                         userLabels.erase(lookup[0]->getLabel());
 279
 280                                         if ((lookup.size() > 4) && (!perm)){
 281                                                 m->mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 282                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 283
 284                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 285                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 286
 287                                         }else if ((lookup.size() > 4) && (perm)) {
 288                                                 set< set<int> >::iterator it3;
 289                                                 set<int>::iterator it2;
 290                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 291
 292                                                         set<int> poss = *it3;
 293                                                         vector<SharedRAbundVector*> subset;
 294                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 295
 296                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 297                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 298                                                 }
 299                                         }else {
 300                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 301                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 302                                         }
 303
 304                                         //restore real lastlabel to save below
 305                                         lookup[0]->setLabel(saveLabel);
 306                                 }
 307
 308
 309                                 lastLabel = lookup[0]->getLabel();
 310
 311                                 //get next line to process
 312                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 313                                 lookup = input->getSharedRAbundVectors();
 314                         }
 315
 316                         if (m->control_pressed) {
 317                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 318                                         globaldata->Groups.clear();
 319                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 320                                         return 0;
 321                         }
 322
 323
 324                         //output error messages about any remaining user labels
 325                         set<string>::iterator it;
 326                         bool needToRun = false;
 327                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 328                                 m->mothurOut("Your file does not include the label " + *it);
 329                                 if (processedLabels.count(lastLabel) != 1) {
 330                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 331                                         needToRun = true;
 332                                 }else {
 333                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 334                                 }
 335                         }
 336
 337                         //run last label if you need to
 338                         if (needToRun == true)  {
 339                                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 340                                         lookup = input->getSharedRAbundVectors(lastLabel);
 341
 342                                         m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
 343                                         processedLabels.insert(lookup[0]->getLabel());
 344                                         userLabels.erase(lookup[0]->getLabel());
 345
 346                                         if ((lookup.size() > 4) && (!perm)){
 347                                                 m->mothurOut("Error: Too many groups chosen.  You may use up to 4 groups with the venn command.  I will use the first four groups in your groupfile. If you set perm=t, I will find all possible combos of 4 groups."); m->mothurOutEndLine();
 348                                                 for (int i = lookup.size(); i > 4; i--) { lookup.pop_back(); } //no memmory leak because pop_back calls destructor
 349
 350                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 351                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 352
 353                                         }else if ((lookup.size() > 4) && (perm)) {
 354                                                 set< set<int> >::iterator it3;
 355                                                 set<int>::iterator it2;
 356                                                 for (it3 = combosOfFour.begin(); it3 != combosOfFour.end(); it3++) {
 357
 358                                                         set<int> poss = *it3;
 359                                                         vector<SharedRAbundVector*> subset;
 360                                                         for (it2 = poss.begin(); it2 != poss.end(); it2++) {   subset.push_back(lookup[*it2]);   }
 361
 362                                                         vector<string> outfilenames = venn->getPic(subset, vennCalculators);
 363                                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 364                                                 }
 365                                         }else {
 366                                                 vector<string> outfilenames = venn->getPic(lookup, vennCalculators);
 367                                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 368                                         }
 369
 370                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 371                         }
 372
 373
 374                         //reset groups parameter
 375                         globaldata->Groups.clear();
 376
 377                         if (m->control_pressed) {
 378                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 379                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 380                                         return 0;
 381                         }
 382
 383
 384                 }else{
 385
 386                         while((sabund != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 387
 388                                 if (m->control_pressed) {
 389                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 390                                         delete sabund;
 391                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 392                                         return 0;
 393                                 }
 394
 395                                 if(allLines == 1 || labels.count(sabund->getLabel()) == 1){
 396
 397                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 398                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 399                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 400
 401
 402                                         processedLabels.insert(sabund->getLabel());
 403                                         userLabels.erase(sabund->getLabel());
 404                                 }
 405
 406                                 if ((m->anyLabelsToProcess(sabund->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 407                                         string saveLabel = sabund->getLabel();
 408
 409                                         delete sabund;
 410                                         sabund = input->getSAbundVector(lastLabel);
 411
 412                                         m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 413                                         vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 414                                         for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 415
 416
 417                                         processedLabels.insert(sabund->getLabel());
 418                                         userLabels.erase(sabund->getLabel());
 419
 420                                         //restore real lastlabel to save below
 421                                         sabund->setLabel(saveLabel);
 422                                 }
 423
 424                                 lastLabel = sabund->getLabel();
 425
 426                                 delete sabund;
 427                                 sabund = input->getSAbundVector();
 428                         }
 429
 430                         if (m->control_pressed) {
 431                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 432                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 433                                         return 0;
 434                         }
 435
 436                         //output error messages about any remaining user labels
 437                         set<string>::iterator it;
 438                         bool needToRun = false;
 439                         for (it = userLabels.begin(); it != userLabels.end(); it++) {
 440                                 m->mothurOut("Your file does not include the label " + *it);
 441                                 if (processedLabels.count(lastLabel) != 1) {
 442                                         m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
 443                                         needToRun = true;
 444                                 }else {
 445                                         m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
 446                                 }
 447                         }
 448
 449                         //run last label if you need to
 450                         if (needToRun == true)  {
 451                                 if (sabund != NULL) {   delete sabund;  }
 452                                 sabund = input->getSAbundVector(lastLabel);
 453
 454                                 m->mothurOut(sabund->getLabel()); m->mothurOutEndLine();
 455                                 vector<string> outfilenames = venn->getPic(sabund, vennCalculators);
 456                                 for(int i = 0; i < outfilenames.size(); i++) { if (outfilenames[i] != "control" ) { outputNames.push_back(outfilenames[i]); }  }
 457
 458                                 delete sabund;
 459
 460                         }
 461
 462                         if (m->control_pressed) {
 463                                         for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 464                                         for (int i = 0; i < outputNames.size(); i++) {  remove(outputNames[i].c_str());  }
 465                                         return 0;
 466                         }
 467                 }
 468
 469                 for (int i = 0; i < vennCalculators.size(); i++) {      delete vennCalculators[i];      }
 470
 471                 m->mothurOutEndLine();
 472                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 473                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 474                 m->mothurOutEndLine();
 475
 476
 477                 return 0;
 478         }
 479         catch(exception& e) {
 480                 m->errorOut(e, "VennCommand", "execute");
 481                 exit(1);
 482         }
 483 }
 484 //**********************************************************************************************************************
 485 //returns a vector of sets containing the 4 group combinations
 486 set< set<int> > VennCommand::findCombinations(int lookupSize){
 487         try {
 488                 set< set<int> > combos;
 489
 490                 set<int> possibles;
 491                 for (int i = 0; i < lookupSize; i++) {  possibles.insert(i);  }
 492
 493                 getCombos(possibles, combos);
 494
 495                 return combos;
 496
 497         }
 498         catch(exception& e) {
 499                 m->errorOut(e, "VennCommand", "findCombinations");
 500                 exit(1);
 501         }
 502 }
 503 //**********************************************************************************************************************
 504 //recusively finds combos of 4
 505 int VennCommand::getCombos(set<int> possibles, set< set<int> >& combos){
 506         try {
 507
 508                 if (possibles.size() == 4) { //done
 509                         if (combos.count(possibles) == 0) { //no dups
 510                                 combos.insert(possibles);
 511                         }
 512                 }else { //we still have work to do
 513                         set<int>::iterator it;
 514                         set<int>::iterator it2;
 515                         for (it = possibles.begin(); it != possibles.end(); it++) {
 516
 517                                 set<int> newPossibles;
 518                                 for (it2 = possibles.begin(); it2 != possibles.end(); it2++) {  //all possible combos of one length smaller
 519                                         if (*it != *it2) {
 520                                                 newPossibles.insert(*it2);
 521                                         }
 522                                 }
 523                                 getCombos(newPossibles, combos);
 524                         }
 525                 }
 526
 527                 return 0;
 528         }
 529         catch(exception& e) {
 530                 m->errorOut(e, "VennCommand", "getCombos");
 531                 exit(1);
 532         }
 533 }
 534
 535 //**********************************************************************************************************************